I need to add some substitution models into PAML (e.g. BLOSUM62, RtREV, VT). Is there anywhere I can download these from, ideally in .dat format?
Thanks for your help.
1) For PAM250
2 For BLOSUM62
3) For Rt REV Matrices
4) For VT Matrices
5) A very good article regarding substitutional Matrices
Hope this helps
There was an issue with BLOSUM 62. Be sure you get the 'correct' BLOSUM series of substitution tables
You can try this web site : http://www.genome.jp/aaindex/
You'll find about 90 substitution matrices with the publication related.
It's an old resource but still full of many references.